The ground- and excited-state interactions of N-(2-ethanoic acid)- 1,8-naphthalimide (NI-ala), along with tryptophan and tyrosine- substituted 1,8-naphthalimide derivatives (NI-trp and NI-tyr), with amino acids and native proteins have been studied in aqueous buffered solution. The singlet excited state of NI-ala reacts with the aromatic amino acids, tryptophan, tyrosine, and histidine with a rate constant at or exceeding the diffusion-controlled limit. Reactivity with bovine serum albumin (BSA) and lysozyme was also demonstrated. However, in all cases, no long-lived redox products were observed from the singlet state quenching. The reactivity of the triplet excited state of NI-ala with the individual amino acids and proteins was studied using laser flash photolysis. Triplet-state reactivity was demonstrated with tryptophan and tyrosine, along with BSA and lysozyme proteins. In the case of tryptophan, tyrosine, and lysozyme, long-lived redox products were observed and quantified. Neutral tryptophan and tyrosyl radicals were observed by transient spectroscopy as quenching products. Upon photolysis of all three 1,8-naphthalimide derivatives, both cleavage and cross-linking of the lysozyme are observed. These studies have identified the potential oxidative targets in native proteins and demonstrated the utility of our naphthalimide derivatives to photomodify native proteins.